The content value chain

Literate Programming

I tried many tools for Literate Programming

The content pipeline for .ipynb

About 75% of data scientists use Python through Jupyter notebooks, and one can use pandoc to generate papers and PowerPoint, but it can be complicated.

graph LR
    A[.ipynb] --> B(("Pandoc"))
    B ----> E[.doc]
    B ----> H[.pptx]
    B --> C[.md]
    B --> D[.tex] 
    D --> F((Xetex))
    C --> I((Hugo))
    F --> G[.pdf]
    I --> J[.html]
    style B fill:#FF6655AA
    style F fill:#88ffFF
    style I fill:#88ffFF

Quarto for Python, in a nutshell

In Quarto’s .qmd files, you write Markdown and code, just like .ipynb. Add some YAML configuration and Quarto does the intermediate steps. It integrates well with VSCode and Jupyter.

graph LR
Q[.qmd] --> A
subgraph Quarto
    A[.ipynb] --> B(("Pandoc"))
    B --> C[.md]
    B --> D[.tex] 
    D --> F((Xetex))
    C --> I((Hugo))
    style B fill:#FF6655AA
    style F fill:#88ffFF
    style I fill:#88ffFF
end
    B ----> E[.doc]
    B ----> H[.pptx]
    F --> G[.pdf]
    I --> J[.html]

But wait, there’s more!

Quarto can easily run pre-scripts and post-scripts. I frequenly use this to pre-process data and to automatically publish output to git repositories.

graph LR
    P[Pre-scripts] --> Q
    style P fill:#AA99FF
    Q[.qmd] --> A
    subgraph Quarto
        A[.ipynb] --> B(("Pandoc"))
        B --> C[.md]
        B --> D[.tex] 
        D --> F((Xetex))
        C --> I((Hugo))
        style B fill:#FF6655AA
        style F fill:#88ffFF
        style I fill:#88ffFF
    end
        B ----> E[.doc]
        B ----> H[.pptx]
        F --> G[.pdf]
        I --> J[.html]
    E --> X[Post-scripts]
    H --> X
    G --> X
    J --> X
    style X fill:#AA99FF

The YAML front-matter

---
title: "Using Quarto for everything"
format: 
    pptx:
        reference-doc: templates/template.pptx
    revealjs:
        incremental: false
        theme: pulse

author: Lucas A. Meyer
date: 2022-07-07
---

Main content

### Writing the main content

Most writing in Quarto is done in [Markdown].

Quarto's Markdown supports everything I'm
used to: figures, tables, bibliography, etc.

It also supports lots of extra features, like
diagrams with `mermaid` and `GraphViz` and
even LaTeX equations: 

$$
E = mc^2
$$

What if I want to add code?

import numpy as np
import matplotlib.pyplot as plt

r = np.arange(0, 2, 0.01)
theta = 2 * np.pi * r
fig, ax = plt.subplots(subplot_kw=\
                {'projection': 'polar'})
ax.plot(theta, r)
ax.set_rticks([0.5, 1, 1.5, 2])
ax.grid(True)
plt.show()

Diagrams

flowchart LR

A[Hard] -->|Text| B(Round)
B --> C{Decision}
C -->|One| D[Result 1]
C -->|Two| E[Result 2]

flowchart LR

A[Hard] -->|Text| B(Round)
B --> C{Decision}
C -->|One| D[Result 1]
C -->|Two| E[Result 2]

Regression and results

# Load the data
df_wage = pd.read_csv("data/wage1.csv")

# Create an OLS model using the R syntax - assumes an intercept
mod = smf.ols(formula="wage ~ educ",
              data=df_wage)

# Fit the model
res = mod.fit()

# Show the results
display(Markdown(md(res.summary().
        tables[1].as_html())))

Basic slide syntax

To create slides, you create sections 
with `#`, titles with `##`, and bullets 
with `-`.

Quarto will render your content in slide form.

### Content types

- You can add several types of content
    - code (use backticks)
    - images
    - diagrams
    - tables
    - etc.

Creating PowerPoint slides

PowerPoint layout rules

The rules are available at:
https://pandoc.org/MANUAL.html#powerpoint-layout-choice

• Title Slide: created from metadata fields like title and author
• Section Header: created from the top-level markdown headings (for example, #)
• Two Content: used when .md source contains .columns div (:::: {.columns}) and text content
• Comparison: same as “Two Content”, but content of divs is not text
• Blank: used for slides that have no displayable content (e.g. notes)
• Content with Caption: used when content doesn’t have a columns div but has text and non-text content
• Title and Content: whatever doesn’t fit the rules above.

PowerPoint templates

By adding a reference-doc entry to your YAML, you can tell Quarto (and pandoc) to use a file as a template for the format of your presentation.

The “Slide Master” needs to contain layouts named as per the previous slide (e.g. “Comparison”).

This allows you a lot of flexibility in the design of your slide deck, even if it is for just the small number of layouts that were listed in the previous slide.

You can control fonts, add background images, page numbering, etc.

---
title: "Using Quarto for everything"
format: pptx
reference-doc: templates/template.pptx
author: Lucas A. Meyer
date: 2022-07-14
---

Best feature: generate content dynamically

Let’s say you’re presenting a project about population dynamics but you don’t know which world leaders are coming to the conference.

On the presentation day, you learn that Belgium, China, Brazil, India, Japan and Nigeria are attending.

You can use Python or R to automatically generate slides.

Generating slides with Python

The next slides/sections were generated using the code below:

df_dr = pd.read_csv("data/dr.csv.gz", compression="gzip")
df_pop = pd.read_csv("data/pop_brackets.csv.gz", compression="gzip")

years = [2000, 2025, 2050, 2075, 2100]
regions = ["Belgium", "China", "Brazil", "India", "Japan", "Nigeria"]

for name in regions:
    display(Markdown(f"## Age and Population Pyramids for {name}"))
    display(Markdown(f'<div class="columns">'))
    display(Markdown(f'<div class="column">'))
    plot_dependency_ratio(df_dr[df_dr.Location == name])
    display(Markdown(f'</div>'))
    display(Markdown(f'<div class="column">'))
    plot_population_pyramid_series(df_pop[df_pop["Location"]==name], years)
    display(Markdown(f'</div>'))
    display(Markdown(f'</div>'))

Age and Population Pyramids for Belgium

Age and Population Pyramids for China

Age and Population Pyramids for Brazil

Age and Population Pyramids for India

Age and Population Pyramids for Japan

Age and Population Pyramids for Nigeria

What I could get by just changing the format in YAML

---
title: "Using Quarto for everything"
format: html
    # revealjs:
    #     incremental: false
    #     theme: [simple, revealjs-customizations.scss]
    #     title-slide-attributes:
    #         data-background-image: images/data-viz-bg.jpg
    #         data-background-size: contain
    #         data-background-position: right

author: Lucas A. Meyer
date: 2022-07-14
---

Adding or changing the format to html will create a website.

Screenshot of website

Generating a scholarly article

I reused some of the content of this presentation to create two scholarly-looking articles. The purpose of the articles is just to show how easy it is to generate them with Quarto, they don’t contain original research.

The relevant files are:

• Quarto source file
• Microsoft Word output
• LaTeX PDF output

Scholarly article screenshots

Citations and Footnotes

Citations don’t work on presentations, but are easy to add to documents.

You need a BibTex file, e.g., bibliography.bib, and a reference to it bibliography: references.bib to the YAML front-matter. Quarto supports any Citation Style Language.

You can cite by using [@citation-name] in your text. Please check the article .qmd source and the PDF and DOCX outputs.

Generating footnotes is also easy. Using [^ref] links to a footnote, and [^ref: content of the footnote] generates its content¹.

Books in Quarto

Here are few books that have been recently written with Quarto:

Where I think Quarto is good (July 2022)